The nuclear architecture and its cancer-related changes have been studied since Boveri first postulated that the nuclear architecture differs between normal and cancer cells [Boveri, 1914; Boveri, 2008]. Over the course of the last century the structure of DNA has been unraveled at various length scales. The structure by itself does not, however, reveal its spatial organization within the nucleus. Many current models about the nuclear architecture are studied in animals and human cell lines. For clinical applications such models also need to be validated in primary human tumor cells.
Chromosomes occupy distinct regions in the interphase nucleus, designated as chromosome territories (CTs) [Cremer and Cremer, 2006a; Cremer and Cremer, 2006b]. The position of each human CT inside the nucleus is determined by its size and gene density [Tanabe et al., 2002]. As the spatial distribution of DNA is non-random, it is important to assess the spatial DNA structure. This would include measurements at length scales larger than the typical sizes of the quaternary nucleic acid structure.
Microscopic analyses of the DNA structure in cell nuclei have been performed since the wide-scale availability of digital image processing. Automatic estimation of the number of low and high density DNA regions within a white blood cell has been performed since the 1980s [Bins et al., 1981].
It has also been noted that chromatin is structurally organized on various length scales that can be made visible using light microscopy [Einstein et al., 1998]. Differences in the microscopic DNA structure have been described using various names, including chromatin condensation, chromatin structure and chromosome packaging, in a variety of diseases, including cancer [Hannen et al., 1998; Natarajan et al., 2012; Vergani et al., 1999].
3D structured illumination microscopy (3D-SIM) is a superresolution imaging modality that has only recently found its way to the biology laboratory. This methodology offers a higher image resolution than conventional epifluorescence widefield microscopy through the use of heterodyne detection of a fluorescent sample illuminated by a periodic pattern [Cragg and So, 2000; Frohn et al., 2000; Gustafsson, 2000; Heintzmann and Cremer, 1999]. 3D-SIM images of DNA, stained with DAPI, reveal nuclear pore protein complex features that had not been seen with conventional microscopy methods [Schermelleh et al., 2008]. Investigation of the nuclear architecture using FISH (fluorescent in situ hybridization) showed that, during FISH experiments, key characteristics of the ultrastructure are preserved [Markaki et al., 2012].